Hi Gerard,
we don't really use the parcellation-based cc measures anymore, but
rather the ones in the aseg.mgz. Those aren't lateralized, but are broken
up into poster/anterior segments.
cheers
Bruce
On Mon, 16 Nov 2009, Freesurfer Local Archive wrote:
> Dear Freesurfers,
>
> I was wondering
Dear Freesurfers,
I was wondering if there is any way to compute volumes of the CC_*
callosal patitions separately for left and right hemispheres? I
noticed that there are separate labels for the left and right lateral
portions of the corpus callosum (e.g. ctx-lh-corpuscallosum vs.
ctx-rh-corpusca
I would try using the norm.mgz or the nu.mgz if you think the norm is too
processed. The orig.mgz is the 001 sampled into 256^3 and 1mm iso
8bits/voxel
On Mon, 16 Nov 2009, Jared Price wrote:
> I guess I am not entirely sure what the contrast properties of orig.mgz
> are. After looking at the
There is a little bit of intensity normalization in the orig.mgz. You
can convert the 001.mgz to anatomical space with mri_vol2vol, something like
mri_vol2vol --mov orig/001.mgz --targ orig.mgz --regheader --o 001.anat.mgz
Jared Price wrote:
> I guess I am not entirely sure what the contrast pro
I guess I am not entirely sure what the contrast properties of orig.mgz
are. After looking at the recon-all DevTable I don't see anything that
explicitly mentions any intensity normalization occurring before this
point so I imagine it would work. I guess I will just ask you for your
suggesti
why don't you use the orig.mgz?
On Mon, 16 Nov 2009, Jared Price wrote:
> Hi all,
> I want to do a manual segmentation of the putamen in tkmedit, but rather
> than using brainmask.mgz as the main volume, I wanted to use 001.mgz.
> This is because the intensity normalization step can in certain cas
Does the orig.mgz have contrast properties that you can use?
Jared Price wrote:
> Hi all,
> I want to do a manual segmentation of the putamen in tkmedit, but rather
> than using brainmask.mgz as the main volume, I wanted to use 001.mgz.
> This is because the intensity normalization step can i
Hi all,
I want to do a manual segmentation of the putamen in tkmedit, but rather
than using brainmask.mgz as the main volume, I wanted to use 001.mgz.
This is because the intensity normalization step can in certain cases
brighten lighter areas of the putamen to 110. Anyway, when I load the
00
Probably something wrong in your contrast files.
It's hard to tell just from this msg
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
--- Novo Netfilter 3.2 www.Netfilter.com.br
--- Novo Netfilter Smal
What probably happened is that you ran QDEC a couple of times. The
currently distributed version does not clean up very well and leaves
files from old analyses around. You may need to delete the qdec
directory and re-run it.
doug
Dalwani, Manish wrote:
> Hi All,
>
> I am getting the following
Hi All,
I am getting the following error after running the simulation script generated
by QDEC.
ERROR: dimension mismatch between X and contrast
/usr/local/freesurfer/subjects/
qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has 2
cols, C has 6 cols
Kindly advise!
Regar
Hi All,
I am getting the following error after running the simulation script generated
by QDEC.
ERROR: dimension mismatch between X and contrast
/usr/local/freesurfer/subjects/
qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has
2 cols, C has 6 cols
Kindly advise!
Hi All,
I am getting the following error after running the simulation script generated
by QDEC.
ERROR: dimension mismatch between X and contrast
/usr/local/freesurfer/subjects/
qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has
2 cols, C has 6 cols
Kindly advise!
not trivially, although it would be easy to do the replacement in matlab.
It's because it binarizes the labels to 128 (which is Nerve in our LUT)
On
Mon, 16 Nov 2009, Jared Price wrote:
> Thanks, I tried mri_extract_label and it works fine. However, it
> extracts the structure and gives it the
I don't know about extract_label, but you can set the output value in
mri_binarize
Jared Price wrote:
> Thanks, I tried mri_extract_label and it works fine. However, it
> extracts the structure and gives it the label "nerve". Is there any way
> within mri_extract_label to keep the original l
Thanks, I tried mri_extract_label and it works fine. However, it
extracts the structure and gives it the label "nerve". Is there any way
within mri_extract_label to keep the original labels (i.e. left putamen,
right putamen, or whatever)?
Jared
___
Try mri_binarize with the --match option. Look in FreeSurferColorLUT.txt
for the match numbers to use.
doug
Jared Price wrote:
> Anyone know how to extract a single structure from aseg.mgz? In other
> words I assume it is possible to use the information in aseg.mgz to
> extract a single struc
mri_extract_label or mri_binarize will do it
On Mon, 16 Nov 2009, Jared
Price wrote:
> Anyone know how to extract a single structure from aseg.mgz? In other
> words I assume it is possible to use the information in aseg.mgz to
> extract a single structure such that there is a new.mgz file that
>
Anyone know how to extract a single structure from aseg.mgz? In other
words I assume it is possible to use the information in aseg.mgz to
extract a single structure such that there is a new.mgz file that
contains just the segmentation of the putamen or just of the caudate or
whatever. Thanks.
Try adding $FREESURFER_HOME/fsfast/bin to your path.
doug
Anna Rotarska-Jagiela wrote:
>
>
> Dear Freesurfer Users,
> during the creation of average brain with Freesurfer, I got the
> following ERROR message:
> > > getpwdcmd: command not found
> > > ERROR: format for rh.orig.avg.area.mgh not re
The 2nd step only creates a mask of the entire surface. You need a step
3 in which you multiply them together:
3. mris_calc -o product.mgz lobe.mgz mul lobe_surface.mgz
Martin Ystad wrote:
> I tried this, but something is going wrong. Here's what I did:
> 1. I ran $ mri_binarize --i subjid/mri/
I tried this, but something is going wrong. Here's what I did:
1. I ran $ mri_binarize --i subjid/mri/aparc+asec.mgz --match xx --match
yy --o lobe.mgz
- this produces a nice binary mask of, say, the left frontal lobe.
2. Then I ran $ mri_surf2vol --mkmask --surf pial --hemi lh --template
lobe.mg
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